src/01_build_list.py

#!/usr/bin/env python3
"""
Scan pieces/2026_01_26 for cullpdb_* list and .fasta pairs. Writes:
1) cullpdb_list_fasta_index.csv - paired only, with full paths
2) cullpdb_full_compiled_list.csv - every list and every fasta found (full compiled list)
"""
import csv
import re
from pathlib import Path
from typing import Optional

SCRIPT_DIR = Path(__file__).resolve().parent
BASE = SCRIPT_DIR.parent
CULLPDB_DIR = BASE / "pieces" / "2026_01_26"
CURATED_DIR = BASE / "curated_csv"
OUT_CSV = CURATED_DIR / "cullpdb_list_fasta_index.csv"
FULL_LIST_CSV = CURATED_DIR / "cullpdb_full_compiled_list.csv"

# cullpdb_pc20.0_res0.0-1.0_noBrks_len40-10000_R0.2_Xray_d2026_01_26_chains300
PAT = re.compile(
    r"^cullpdb_pc([\d.]+)_res([\d.]+)-([\d.]+)_"
    r"(?:(noBrks)_)?"
    r"len40-10000_R([\d.]+)_"
    r"(.+?)_d\d{4}_\d{2}_\d{2}_chains(\d+)$"
)


def parse_basename(name: str) -> Optional[dict]:
    base = name.removesuffix(".fasta")
    m = PAT.match(base)
    if not m:
        return None
    pc, res_min, res_max, no_brks, r_cutoff, methods, n_chains = m.groups()
    n = int(n_chains)
    no_brk = no_brks is not None
    return {
        "list_basename": base,
        "fasta_basename": base + ".fasta",
        "n_chains": n,
        "pc": float(pc),
        "resolution": f"{res_min}-{res_max}",
        "no_breaks": "yes" if no_brk else "no",
        "R": float(r_cutoff),
        "Nmethods": methods,
    }


def main():
    dir_path = Path(CULLPDB_DIR)
    if not dir_path.is_dir():
        print(f"Missing cullpdb dir: {dir_path}")
        return
    dir_path = dir_path.resolve()
    # Collect every basename that has a list and/or fasta
    bases = set()
    for p in dir_path.iterdir():
        if not p.is_file():
            continue
        name = p.name
        if not name.startswith("cullpdb_") or "len40-10000" not in name:
            continue
        base = name.removesuffix(".fasta")
        bases.add(base)

    # Full compiled list: one row per basename, list path + fasta path (full), and parsed params
    full_rows = []
    paired_rows = []
    for base in sorted(bases):
        list_path = dir_path / base
        fasta_path = dir_path / (base + ".fasta")
        list_exists = list_path.exists()
        fasta_exists = fasta_path.exists()
        parsed = parse_basename(base)
        if not parsed:
            full_rows.append({
                "list_basename": base,
                "fasta_basename": base + ".fasta",
                "list_path": str(list_path) if list_exists else "",
                "fasta_path": str(fasta_path) if fasta_exists else "",
                "list_exists": list_exists,
                "fasta_exists": fasta_exists,
                "paired": list_exists and fasta_exists,
                "n_chains": "",
                "pc": "",
                "resolution": "",
                "no_breaks": "",
                "R": "",
                "Nmethods": "",
            })
            continue
        row_full = {
            "list_basename": base,
            "fasta_basename": base + ".fasta",
            "list_path": str(list_path) if list_exists else "",
            "fasta_path": str(fasta_path) if fasta_exists else "",
            "list_exists": list_exists,
            "fasta_exists": fasta_exists,
            "paired": list_exists and fasta_exists,
            "n_chains": parsed["n_chains"],
            "pc": parsed["pc"],
            "resolution": parsed["resolution"],
            "no_breaks": parsed["no_breaks"],
            "R": parsed["R"],
            "Nmethods": parsed["Nmethods"],
        }
        full_rows.append(row_full)
        if list_exists and fasta_exists:
            paired_rows.append({
                "list_basename": base,
                "fasta_basename": base + ".fasta",
                "list_path": str(list_path),
                "fasta_path": str(fasta_path),
                "n_chains": parsed["n_chains"],
                "pc": parsed["pc"],
                "resolution": parsed["resolution"],
                "no_breaks": parsed["no_breaks"],
                "R": parsed["R"],
                "Nmethods": parsed["Nmethods"],
            })

    CURATED_DIR.mkdir(parents=True, exist_ok=True)
    # 1) Paired index with full paths
    fieldnames = [
        "list_basename", "fasta_basename", "list_path", "fasta_path",
        "n_chains", "pc", "resolution", "no_breaks", "R", "Nmethods",
    ]
    with open(OUT_CSV, "w", newline="") as f:
        w = csv.DictWriter(f, fieldnames=fieldnames)
        w.writeheader()
        w.writerows(paired_rows)
    print(f"Wrote {OUT_CSV} with {len(paired_rows)} list↔fasta pairs (full paths).")

    # 2) Full compiled list: every basename, list/fasta paths and exists flags
    full_fieldnames = [
        "list_basename", "fasta_basename", "list_path", "fasta_path",
        "list_exists", "fasta_exists", "paired",
        "n_chains", "pc", "resolution", "no_breaks", "R", "Nmethods",
    ]
    with open(FULL_LIST_CSV, "w", newline="") as f:
        w = csv.DictWriter(f, fieldnames=full_fieldnames)
        w.writeheader()
        w.writerows(full_rows)
    n_paired = sum(1 for r in full_rows if r["paired"])
    print(f"Wrote {FULL_LIST_CSV} with {len(full_rows)} entries (full compiled list); {n_paired} paired.")


if __name__ == "__main__":
    main()